ISDA

Deposition Date 2016-05-28

Release Date 2016-12-14

Last Version Date 2024-05-01

Entry Detail

PDB ID:

5L57

Keywords:

OXIDOREDUCTASE

Title:

Crystal structure of Iso-citrate Dehydrogenase R132H in complex with a novel inhibitor (compound 13a)

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 43 21 2

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Isocitrate dehydrogenase [NADP] cytoplasmic
Gene (Uniprot):IDH1
Chain IDs:A
Chain Length:414
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O75874 Pfam ID:PF00180 EC:1.1.1.42

Ligand Molecules

6N3

NDP

Primary Citation

Discovery and Optimization of Allosteric Inhibitors of Mutant Isocitrate Dehydrogenase 1 (R132H IDH1) Displaying Activity in Human Acute Myeloid Leukemia Cells.

Jones, S, Ahmet, J, Ayton, K, Ball, M, Cockerill, M, Fairweather, E, Hamilton, N, Harper, P, Hitchin, J, Jordan, A, Levy, C, Lopez, R, McKenzie, E, Packer, M, Plant, D, Simpson, I, Simpson, P, Sinclair, I, Somervaille, T.C, Small, H, Spencer, G.J, Thomson, G, Tonge, M, Waddell, I, Walsh, J, Waszkowycz, B, Wigglesworth, M, Wiseman, D.H, Ogilvie, D.Show

J.Med.Chem. 59 11120 11137 (2016)

PMID: 28002956 DOI: 10.1021/acs.jmedchem.6b01320

Abstact

A collaborative high throughput screen of 1.35 million compounds against mutant (R132H) isocitrate dehydrogenase IDH1 led to the identification of a novel series of inhibitors. Elucidation of the bound ligand crystal structure showed that the inhibitors exhibited a novel binding mode in a previously identified allosteric site of IDH1 (R132H). This information guided the optimization of the series yielding submicromolar enzyme inhibitors with promising cellular activity. Encouragingly, one compound from this series was found to induce myeloid differentiation in primary human IDH1 R132H AML cells in vitro.

Legend

Protein

Chemical

Disease

Primary Citation of related structures